Loading report..

Highlight Samples

This report has flat image plots that won't be highlighted.
See the documentation for help.

Regex mode off

    Rename Samples

    This report has flat image plots that won't be renamed.
    See the documentation for help.

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      This report has flat image plots that won't be hidden.
      See the documentation for help.

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.


        Load Settings

        Choose a saved report profile from the dropdown box below:

        About MultiQC

        This report was generated using MultiQC, version 1.10.1

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2021-07-26, 17:44 based on data in: /data/SBCS-EizaguirreLab/Alice/StickParaBroOff/QualityControl/QC01_TrimmedReads_fastqc


        General Statistics

        Showing 144/144 rows and 4/5 columns.
        Sample Name% Dups% GCLengthM Seqs
        G04873-L1_S1_L001_R1_001_trimmed_cutadapt
        70.9%
        32%
        93 bp
        10.8
        G04874-L1_S2_L001_R1_001_trimmed_cutadapt
        73.9%
        33%
        95 bp
        10.0
        G04875-L1_S3_L001_R1_001_trimmed_cutadapt
        73.1%
        31%
        95 bp
        11.1
        G04876-L1_S4_L001_R1_001_trimmed_cutadapt
        71.4%
        32%
        95 bp
        11.5
        G04877-L1_S5_L001_R1_001_trimmed_cutadapt
        70.9%
        32%
        95 bp
        11.2
        G04878-L1_S6_L001_R1_001_trimmed_cutadapt
        71.8%
        32%
        95 bp
        11.5
        G04879-L1_S7_L001_R1_001_trimmed_cutadapt
        69.7%
        31%
        95 bp
        8.2
        G04880-L1_S8_L001_R1_001_trimmed_cutadapt
        72.7%
        32%
        94 bp
        9.4
        G04881-L1_S9_L001_R1_001_trimmed_cutadapt
        75.5%
        33%
        94 bp
        14.3
        G04882-L1_S10_L001_R1_001_trimmed_cutadapt
        72.7%
        31%
        95 bp
        12.0
        G04883-L1_S11_L001_R1_001_trimmed_cutadapt
        77.0%
        31%
        96 bp
        12.9
        G04884-L1_S12_L001_R1_001_trimmed_cutadapt
        81.8%
        34%
        82 bp
        5.8
        G04885-L1_S13_L001_R1_001_trimmed_cutadapt
        73.1%
        31%
        96 bp
        10.0
        G04886-L1_S14_L001_R1_001_trimmed_cutadapt
        71.1%
        31%
        95 bp
        10.5
        G04887-L1_S15_L001_R1_001_trimmed_cutadapt
        69.6%
        31%
        95 bp
        8.3
        G04888-L1_S16_L001_R1_001_trimmed_cutadapt
        72.3%
        31%
        95 bp
        10.5
        G04889-L1_S17_L001_R1_001_trimmed_cutadapt
        74.4%
        33%
        95 bp
        9.2
        G04890-L1_S18_L001_R1_001_trimmed_cutadapt
        72.7%
        33%
        95 bp
        9.5
        G04891-L1_S19_L002_R1_001_trimmed_cutadapt
        73.2%
        32%
        95 bp
        11.3
        G04892-L1_S20_L002_R1_001_trimmed_cutadapt
        75.4%
        33%
        96 bp
        12.5
        G04893-L1_S21_L002_R1_001_trimmed_cutadapt
        75.1%
        33%
        93 bp
        11.1
        G04894-L1_S22_L002_R1_001_trimmed_cutadapt
        78.4%
        30%
        96 bp
        5.8
        G04895-L1_S23_L002_R1_001_trimmed_cutadapt
        77.2%
        32%
        95 bp
        11.3
        G04896-L1_S24_L002_R1_001_trimmed_cutadapt
        77.8%
        32%
        95 bp
        19.9
        G04897-L1_S25_L002_R1_001_trimmed_cutadapt
        77.2%
        34%
        95 bp
        11.7
        G04898-L1_S26_L002_R1_001_trimmed_cutadapt
        72.6%
        32%
        95 bp
        11.0
        G04899-L1_S27_L002_R1_001_trimmed_cutadapt
        76.1%
        32%
        96 bp
        11.4
        G04900-L1_S28_L002_R1_001_trimmed_cutadapt
        77.6%
        32%
        96 bp
        12.8
        G04901-L1_S29_L002_R1_001_trimmed_cutadapt
        71.8%
        33%
        96 bp
        9.4
        G04902-L1_S30_L002_R1_001_trimmed_cutadapt
        74.3%
        33%
        96 bp
        10.8
        G04903-L1_S31_L002_R1_001_trimmed_cutadapt
        70.1%
        33%
        96 bp
        6.3
        G04904-L1_S32_L002_R1_001_trimmed_cutadapt
        74.2%
        34%
        94 bp
        8.5
        G04905-L1_S33_L002_R1_001_trimmed_cutadapt
        73.8%
        33%
        94 bp
        10.5
        G04906-L1_S34_L002_R1_001_trimmed_cutadapt
        74.0%
        32%
        95 bp
        9.5
        G04907-L1_S35_L002_R1_001_trimmed_cutadapt
        72.7%
        33%
        94 bp
        9.2
        G04908-L1_S36_L002_R1_001_trimmed_cutadapt
        75.0%
        34%
        94 bp
        8.9
        G04909-L1_S37_L003_R1_001_trimmed_cutadapt
        71.5%
        31%
        96 bp
        7.8
        G04910-L1_S38_L003_R1_001_trimmed_cutadapt
        73.4%
        31%
        96 bp
        11.8
        G04911-L1_S39_L003_R1_001_trimmed_cutadapt
        70.7%
        31%
        95 bp
        11.5
        G04912-L1_S40_L003_R1_001_trimmed_cutadapt
        70.4%
        32%
        95 bp
        10.5
        G04913-L1_S41_L003_R1_001_trimmed_cutadapt
        72.8%
        35%
        92 bp
        6.7
        G04914-L1_S42_L003_R1_001_trimmed_cutadapt
        75.6%
        34%
        94 bp
        13.1
        G04915-L1_S43_L003_R1_001_trimmed_cutadapt
        76.0%
        34%
        93 bp
        11.7
        G04916-L1_S44_L003_R1_001_trimmed_cutadapt
        74.6%
        33%
        94 bp
        9.9
        G04917-L1_S45_L003_R1_001_trimmed_cutadapt
        71.6%
        32%
        94 bp
        12.2
        G04918-L1_S46_L003_R1_001_trimmed_cutadapt
        74.7%
        32%
        95 bp
        8.3
        G04919-L1_S47_L003_R1_001_trimmed_cutadapt
        76.1%
        31%
        96 bp
        13.3
        G04920-L1_S48_L003_R1_001_trimmed_cutadapt
        73.4%
        33%
        96 bp
        12.8
        G04921-L1_S49_L003_R1_001_trimmed_cutadapt
        76.6%
        35%
        92 bp
        11.9
        G04922-L1_S50_L003_R1_001_trimmed_cutadapt
        73.3%
        34%
        94 bp
        9.3
        G04923-L1_S51_L003_R1_001_trimmed_cutadapt
        74.3%
        33%
        93 bp
        10.7
        G04924-L1_S52_L003_R1_001_trimmed_cutadapt
        74.1%
        33%
        94 bp
        11.1
        G04925-L1_S53_L003_R1_001_trimmed_cutadapt
        70.8%
        32%
        94 bp
        12.4
        G04926-L1_S54_L003_R1_001_trimmed_cutadapt
        72.4%
        32%
        94 bp
        12.9
        G04927-L1_S55_L004_R1_001_trimmed_cutadapt
        71.1%
        33%
        95 bp
        8.6
        G04928-L1_S56_L004_R1_001_trimmed_cutadapt
        73.9%
        32%
        94 bp
        10.1
        G04929-L1_S57_L004_R1_001_trimmed_cutadapt
        71.6%
        34%
        93 bp
        8.8
        G04930-L1_S58_L004_R1_001_trimmed_cutadapt
        75.2%
        33%
        93 bp
        13.6
        G04931-L1_S59_L004_R1_001_trimmed_cutadapt
        70.2%
        33%
        93 bp
        10.3
        G04932-L1_S60_L004_R1_001_trimmed_cutadapt
        71.6%
        33%
        94 bp
        10.3
        G04933-L1_S61_L004_R1_001_trimmed_cutadapt
        71.2%
        31%
        95 bp
        9.3
        G04934-L1_S62_L004_R1_001_trimmed_cutadapt
        70.9%
        32%
        94 bp
        11.6
        G04935-L1_S63_L004_R1_001_trimmed_cutadapt
        75.5%
        32%
        95 bp
        10.3
        G04936-L1_S64_L004_R1_001_trimmed_cutadapt
        71.0%
        32%
        96 bp
        10.7
        G04937-L1_S65_L004_R1_001_trimmed_cutadapt
        72.5%
        32%
        95 bp
        9.5
        G04938-L1_S66_L004_R1_001_trimmed_cutadapt
        73.0%
        33%
        94 bp
        10.4
        G04939-L1_S67_L004_R1_001_trimmed_cutadapt
        72.5%
        32%
        95 bp
        12.3
        G04940-L1_S68_L004_R1_001_trimmed_cutadapt
        69.0%
        32%
        94 bp
        10.8
        G04941-L1_S69_L004_R1_001_trimmed_cutadapt
        71.8%
        32%
        94 bp
        12.9
        G04942-L1_S70_L004_R1_001_trimmed_cutadapt
        72.3%
        30%
        95 bp
        7.2
        G04943-L1_S71_L004_R1_001_trimmed_cutadapt
        75.3%
        32%
        94 bp
        11.0
        G04944-L1_S72_L004_R1_001_trimmed_cutadapt
        76.0%
        32%
        94 bp
        13.5
        G04945-L1_S73_L005_R1_001_trimmed_cutadapt
        75.8%
        33%
        93 bp
        12.2
        G04946-L1_S74_L005_R1_001_trimmed_cutadapt
        72.2%
        33%
        94 bp
        11.3
        G04947-L1_S75_L005_R1_001_trimmed_cutadapt
        72.0%
        33%
        94 bp
        10.4
        G04948-L1_S76_L005_R1_001_trimmed_cutadapt
        72.8%
        33%
        93 bp
        11.3
        G04949-L1_S77_L005_R1_001_trimmed_cutadapt
        72.6%
        33%
        94 bp
        11.1
        G04950-L1_S78_L005_R1_001_trimmed_cutadapt
        72.8%
        31%
        95 bp
        12.3
        G04951-L1_S79_L005_R1_001_trimmed_cutadapt
        65.6%
        32%
        94 bp
        7.2
        G04952-L1_S80_L005_R1_001_trimmed_cutadapt
        71.4%
        32%
        94 bp
        11.3
        G04953-L1_S81_L005_R1_001_trimmed_cutadapt
        74.7%
        32%
        94 bp
        12.5
        G04954-L1_S82_L005_R1_001_trimmed_cutadapt
        72.3%
        32%
        95 bp
        9.8
        G04955-L1_S83_L005_R1_001_trimmed_cutadapt
        72.7%
        33%
        94 bp
        10.9
        G04956-L1_S84_L005_R1_001_trimmed_cutadapt
        71.6%
        32%
        94 bp
        11.7
        G04957-L1_S85_L005_R1_001_trimmed_cutadapt
        72.1%
        31%
        95 bp
        11.1
        G04958-L1_S86_L005_R1_001_trimmed_cutadapt
        73.7%
        32%
        95 bp
        10.0
        G04959-L1_S87_L005_R1_001_trimmed_cutadapt
        73.0%
        31%
        95 bp
        10.1
        G04960-L1_S88_L005_R1_001_trimmed_cutadapt
        73.7%
        31%
        95 bp
        10.0
        G04961-L1_S89_L005_R1_001_trimmed_cutadapt
        73.5%
        32%
        95 bp
        10.0
        G04962-L1_S90_L005_R1_001_trimmed_cutadapt
        73.4%
        33%
        93 bp
        10.7
        G04963-L1_S91_L006_R1_001_trimmed_cutadapt
        71.4%
        32%
        95 bp
        12.1
        G04964-L1_S92_L006_R1_001_trimmed_cutadapt
        70.1%
        31%
        95 bp
        9.6
        G04965-L1_S93_L006_R1_001_trimmed_cutadapt
        71.1%
        31%
        96 bp
        10.9
        G04966-L1_S94_L006_R1_001_trimmed_cutadapt
        68.9%
        30%
        96 bp
        8.3
        G04967-L1_S95_L006_R1_001_trimmed_cutadapt
        74.7%
        32%
        97 bp
        9.4
        G04968-L1_S96_L006_R1_001_trimmed_cutadapt
        74.0%
        31%
        97 bp
        10.3
        G04969-L1_S97_L006_R1_001_trimmed_cutadapt
        72.5%
        31%
        95 bp
        12.8
        G04970-L1_S98_L006_R1_001_trimmed_cutadapt
        72.3%
        31%
        96 bp
        10.5
        G04971-L1_S99_L006_R1_001_trimmed_cutadapt
        72.4%
        31%
        95 bp
        10.1
        G04972-L1_S100_L006_R1_001_trimmed_cutadapt
        70.6%
        32%
        95 bp
        12.0
        G04973-L1_S101_L006_R1_001_trimmed_cutadapt
        72.8%
        31%
        97 bp
        10.3
        G04974-L1_S102_L006_R1_001_trimmed_cutadapt
        74.6%
        31%
        97 bp
        10.6
        G04975-L1_S103_L006_R1_001_trimmed_cutadapt
        74.4%
        31%
        97 bp
        10.7
        G04976-L1_S104_L006_R1_001_trimmed_cutadapt
        74.8%
        31%
        97 bp
        9.3
        G04977-L1_S105_L006_R1_001_trimmed_cutadapt
        73.2%
        32%
        95 bp
        10.6
        G04978-L1_S106_L006_R1_001_trimmed_cutadapt
        71.9%
        31%
        95 bp
        10.0
        G04979-L1_S107_L006_R1_001_trimmed_cutadapt
        69.9%
        32%
        94 bp
        11.4
        G04980-L1_S108_L006_R1_001_trimmed_cutadapt
        71.9%
        32%
        95 bp
        11.5
        G04981-L1_S109_L007_R1_001_trimmed_cutadapt
        73.3%
        32%
        96 bp
        12.4
        G04982-L1_S110_L007_R1_001_trimmed_cutadapt
        56.7%
        32%
        96 bp
        3.4
        G04983-L1_S111_L007_R1_001_trimmed_cutadapt
        71.2%
        31%
        95 bp
        10.8
        G04984-L1_S112_L007_R1_001_trimmed_cutadapt
        74.9%
        31%
        96 bp
        15.4
        G04985-L1_S113_L007_R1_001_trimmed_cutadapt
        74.3%
        31%
        96 bp
        11.0
        G04986-L1_S114_L007_R1_001_trimmed_cutadapt
        71.7%
        31%
        96 bp
        10.7
        G04987-L1_S115_L007_R1_001_trimmed_cutadapt
        73.1%
        31%
        96 bp
        10.5
        G04988-L1_S116_L007_R1_001_trimmed_cutadapt
        78.0%
        30%
        96 bp
        11.1
        G04989-L1_S117_L007_R1_001_trimmed_cutadapt
        75.8%
        31%
        96 bp
        12.3
        G04990-L1_S118_L007_R1_001_trimmed_cutadapt
        83.1%
        30%
        97 bp
        5.5
        G04991-L1_S119_L007_R1_001_trimmed_cutadapt
        72.7%
        30%
        96 bp
        10.0
        G04992-L1_S120_L007_R1_001_trimmed_cutadapt
        78.5%
        30%
        97 bp
        12.5
        G04993-L1_S121_L007_R1_001_trimmed_cutadapt
        75.4%
        31%
        96 bp
        12.8
        G04994-L1_S122_L007_R1_001_trimmed_cutadapt
        74.3%
        30%
        96 bp
        11.0
        G04995-L1_S123_L007_R1_001_trimmed_cutadapt
        76.0%
        32%
        96 bp
        12.3
        G04996-L1_S124_L007_R1_001_trimmed_cutadapt
        73.6%
        32%
        96 bp
        13.2
        G04997-L1_S125_L007_R1_001_trimmed_cutadapt
        74.2%
        33%
        96 bp
        11.5
        G04998-L1_S126_L007_R1_001_trimmed_cutadapt
        73.9%
        32%
        95 bp
        13.9
        G04999-L1_S127_L008_R1_001_trimmed_cutadapt
        68.7%
        32%
        95 bp
        9.2
        G05000-L1_S128_L008_R1_001_trimmed_cutadapt
        69.8%
        31%
        95 bp
        9.3
        G05001-L1_S129_L008_R1_001_trimmed_cutadapt
        72.2%
        32%
        95 bp
        12.6
        G05002-L1_S130_L008_R1_001_trimmed_cutadapt
        72.5%
        31%
        96 bp
        10.2
        G05003-L1_S131_L008_R1_001_trimmed_cutadapt
        71.4%
        30%
        96 bp
        8.5
        G05004-L1_S132_L008_R1_001_trimmed_cutadapt
        72.9%
        31%
        96 bp
        10.9
        G05005-L1_S133_L008_R1_001_trimmed_cutadapt
        73.2%
        30%
        96 bp
        10.4
        G05006-L1_S134_L008_R1_001_trimmed_cutadapt
        71.1%
        30%
        96 bp
        9.5
        G05007-L1_S135_L008_R1_001_trimmed_cutadapt
        76.0%
        30%
        96 bp
        10.5
        G05008-L1_S136_L008_R1_001_trimmed_cutadapt
        79.1%
        29%
        97 bp
        12.8
        G05009-L1_S137_L008_R1_001_trimmed_cutadapt
        71.5%
        30%
        95 bp
        9.7
        G05010-L1_S138_L008_R1_001_trimmed_cutadapt
        70.4%
        31%
        95 bp
        9.6
        G05011-L1_S139_L008_R1_001_trimmed_cutadapt
        70.9%
        30%
        95 bp
        10.6
        G05012-L1_S140_L008_R1_001_trimmed_cutadapt
        69.1%
        30%
        95 bp
        8.9
        G05013-L1_S141_L008_R1_001_trimmed_cutadapt
        74.7%
        31%
        93 bp
        19.2
        G05014-L1_S142_L008_R1_001_trimmed_cutadapt
        79.7%
        30%
        96 bp
        4.8
        G05015-L1_S143_L008_R1_001_trimmed_cutadapt
        69.7%
        31%
        94 bp
        10.8
        G05016-L1_S144_L008_R1_001_trimmed_cutadapt
        73.5%
        31%
        96 bp
        12.3

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        loading..